Side effects of omeprazole: a system biology study

Aim: To assess the effects of omeprazole on the human cardiovascular system is the main aim of this study. Background: Omeprazole as a proton pump inhibitor is widely consumed to inhibit gastric acid secretion. Methods: Gene expression profiles of “human coronary artery endothelial cells” in the absence and presence of omeprazole were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) interacted as an interactome, and the hub nodes are determined. The DEGs were enriched via gene ontology (GO) analysis. The critical hubs were identified based on the GO findings. Results: Among 103 queried DEGs, 61 individuals were included in the main connected component. CTNNB1, HNRNPA1, SRSF4, TRA2A, SFPQ, and RBM5 genes were identified as critical hub genes. Six clusters of biological terms were introduced as deregulated elements in the presence of omeprazole. Conclusion: In conclusion, long-term consumption of omeprazole may be accompanied with undesirable effects, however more evidence is required.


Introduction
Omeprazole is a proton pump inhibitor applied to inhibit gastric acid secretion (1). There is evidence that omeprazole consumption is accompanied by a few side effects (2). It has been reported that several bone issues occur in patients treated with omeprazole (3). High throughput methods such as proteomics, genomics, and metabolomics have attracted the attention of researchers in the fields of medicine and pharmacology and have led to large amounts of data about drugs and their effects on the human body (4). The large amounts of data imply complex analysis to interpret events and produce useful information. PPI network analysis, which is formed based on the interactions between the studied elements, is a suitable method for screening complex sets of data (5). Many diseases are studied using PPI network analysis, resulting in useful information about their molecular mechanisms (6)(7)(8). GO analysis also is a suitable method for investigating molecular function, cellular components, biological processes, and biochemical pathways related to the studied genes (9,10). In the present study the critical deregulated genes of "human coronary artery endothelial cells" in the presence of omeprazole were determined by PPI network analysis,

ORIGINAL ARTICLE
and GO enrichment was applied to the crucial DEGs to achieve a clear understanding of the effects of omeprazole on the human cardiovascular system.

Methods
Gene expression profiles of GSE77239/GPL570 were download from GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE77239). In this study, the gene expression profiles of 3 cultured "human coronary artery endothelial cells" in the presence of 100 µM omeprazole were compared with cultured cells in the absence of omeprazole as controls (11). The profiles were matched statistically through box plot analysis using GEO2R. The characterized DEGs which had a p-value <0.001, adj. p-value<0.001, and fold change >2, were identified as significant DEGs. The significant DEGs were included in the PPI network through the STRING (12) database by Cytoscape software (13). As only 37 significant DEGs were included in the main connected component of the constructed network, 20 first neighbor genes from the STRING database were added to the queried DEGs to make a maximum participating number of DEGs in the main connected component. The top 10 nodes (among the queried DEGs) based on degree value were considered hub DEGs.
All significant DEGs were enriched through GO analysis by ClueGO and CluePedia (14), two applications of Cytoscape software. Biological terms were clustered according to a kappa score of 0.5. Term p-value, term p-value corrected with Bonferroni step down, group p-value, and group p-value corrected with Bonferroni step down were less than 0.001.

Results
Box plot analysis is shown in Figure 1. GSM2046427-29 as controls and GSM2046433-35 as treated samples were compared. The gene expression profiles are central median and, therefore, statistically comparable.
In total, 103 characterized significant DEGs with logFC>2, p-value <0.001, and adj.  GO results of enrichment of the 103 significant DEGs is shown in Figure 3. Six clusters of biological terms including "adherens junction," "RNA splicing, via transesterification reactions with bulged adenosine as nucleophile," "positive regulation of mitochondrion organization," "cell-substrate adherens junction assembly," "core promoter binding," and "microtubule binding," included 37, 20, 8, 6, 1, and 1 terms, respectively. As seen in Figure 4, the "adherens junction" cluster was associated with 26 DEGs (the brown colored genes) while the second cluster; "RNA splicing, via transesterification reactions with bulged adenosine as nucleophile," was related to 10 genes. The "positive regulation of mitochondrion organization" and "cell-substrate adherens junction assembly" clusters were associated with 5 and 8 DEGs, respectively.    The fifth and sixth clusters were related to 4 and 5 genes, respectively. Considering the common genes, 41 DEGs among 103 queried DEGs were associated with the biological terms. Figure 5 shows the six clusters identified based on frequency of biological terms content of cluster. As can be seen, "adherens junction" was the largest cluster. Details about the six introduced clusters are presented in table 2.

Discussion
Network analysis has attracted the attention of researchers in the fields of medicine and pharmacology due to its abilities in discovering hidden features of applications of common drugs. Omeprazole is known as a common drug used to inhibit acid secretion in gastric disorders (15). Yongning Zhouy et al. reported that omeprazole consumption led to the control of bleeding in 59% of patients with portal hypertensive gastropathy (PHG) after 48 h. PHG is an important problem of liver cirrhosis which contributes to acute gastric bleeding (16). In this study, the role of omeprazole on the function of human coronary artery endothelial cells was studied through the assessment of gene expression profiling. The gene expression profiles were statistically matched, and the significant DEGs were included in the PPI network. Ten hub DEGs were identified and six clusters of deregulated biological terms were determined. The largest cluster "adherens junction," contained 37 biological terms (more than half the total number of terms) is associated with 26 DEGs (63% of the recognized DEGs). The second top hub gene, CTNNB1, was related to the "adherens junction," while HNRNPA1, SRSF4, TRA2A, SFPQ, and RBM5 were associated with the "RNA splicing, via transesterification reactions with bulged adenosine as nucleophile" cluster. Table 2. Details of the six introduced clusters of biological terms. Term p-value, term p-value corrected with Bonferroni step down, group p-value, and group p-value corrected with Bonferroni step down are less than 0.001. G, R, %AG, NG, and AGF refer to group, row, percentage of associated genes, number of genes, and associated genes found, respectively. Names of clusters (the terms that clusters are called with the name of those terms) are bolded.